Persistence and availability of Web services in computational biology

We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72% of Web sites are still available at the published addresses, only 9% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33%, we could not test functionality because there was no example data or a related problem; 13% were truly no longer working as expected; we could positively confirm functionality only for 45% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository.     

Defining ‘periphrasis’: key notions

We examine the notion of ??(inflectional) periphrasis?? within the framework of Canonical Typology, and argue that the canonical approach allows us to define a logically coherent notion of periphrasis. We propose a set of canonical criteria for inflectional morphology and a set of canonical criteria for functional syntax, that is, syntactic constructions which include functional elements and which express grammatical features. We argue that canonical periphrasis is exemplified in our theoretical space of possibilities whenever a cell in a (canonically morphological) inflectional paradigm (??feature intersection??) is expressed by a multiword construction which respects the canonical properties of functional syntax. We compare our canonically-based approach with the approach of other authors, notably, Ackerman & Stump (2004), who argue for three sufficient conditions for a construction to be regarded as periphrastic: feature intersection, non-compositionality and distributed exponence. We argue that non-compositionality and distributed exponence, while sometimes diagnostic of periphrasis on a language-particular basis, do not constitute canonical properties of periphrasis. We also examine crucial but neglected syntactic aspects of periphrastic constructions: recursion of periphrases and headedness of periphrastic constructions. The approach we propose allows us to distinguish between constructions in actual languages which approximate the ideal of canonical periphrasis to various degrees without committing us to a categorical distinction between periphrastic and non-periphrastic constructions. At the same time we can capture the intuition that there is in some languages a distinct identifiable set of multiword constructions whose principal role is to realize grammatical features.     

Stat1 and CD74 overexpression is co-dependent and linked to increased invasion and lymph node metastasis in triple-negative breast cancer

Triple-negative breast cancer is difficult to treat because of the lack of rationale-based therapies. There are no established markers and targets that can be used for stratification of patients and targeted therapy. Here we report the identification of novel molecular features, which appear to augment metastasis of triple negative breast tumors. We found that triple-negative breast tumors can be segregated into 2 phenotypes based on their genome-wide protein abundance profiles. The first is characterized by high expression of Stat1, Mx1, and CD74. Seven out of 9 tumors from this group had invaded at least 2 lymph nodes while only 1 out of 10 tumors in group 2 was lymph node positive. In vitro experiments showed that the interferon-induced increase in Stat1 abundance correlates with increased migration and invasion in cultured cells. When CD74 was overexpressed, it increased cell adhesion on matrigel. This effect was accompanied with a marked increase in the membrane expression of beta-catenin, MUC18, plexins, integrins, and other proteins involved in cell adhesion and cancer metastasis. Taken together, our results show that Stat1/CD74 positive triple-negative tumors are more aggressive and suggest an approach for development of better diagnostics and more targeted therapies for triple negative breast cancer. This article is part of a Special Issue entitled: Proteomics: The clinical link.     

Secondary metabolites and lipids in Chara globularis Thuill

Sterols, volatiles and lipid fatty acids were analysed in the fresh-water alga Chara globularis. Five sterols, two of them new for the genus, were identified, together with 12 fatty acids from lipids. The volatiles appeared to form a complex mixture, containing mainly acids (part of them chlorinated), terpenoids, ketones, hydrocarbons, etc. No flavonoids have been found. Antibacterial activity of extracts has been tested, unpolar extracts showed moderate activity.     

Palaearctic species of the genus Confluaria Ablasov (Cestoda,Hymenolepididae): redescriptions of C. multistriata (Rudolphi, 1810) and C. japonica (Yamaguti, 1935), and a description of Confluaria sp.

Confluaria multistriata (Rudolphi, 1810) is redescribed on the basis of specimens from Tachybaptus ruficollis from the material of Rudolphi and Dollfus and new specimens from the same host species from Bulgaria. The types of C. japonica (Yamaguti, 1935) from T. ruficollis are also redescribed and figured. A single specimen from the collection of Krabbe, described as Taenia multistriata, is re-examined and recognised as belonging to a different species of Confluaria, the status of which remains to be established. Criteria for distinguishing the three species are proposed. In view of the present results, some of the previous records of C. multistriata and C. japonica are re-evaluated. The synonymy of the genera Colymbilepis Spasskaya, 1966 and Confluaria Ablasov in Spasskaya, 1966 is confirmed.     

Taxonomic revision of Tatria Kowalewski, 1904 (Cestoda: Amabiliidae): redescriptions of T. biremis Kowalewski, 1904 and T. minor Kowalewski, 1904, and the description of T. gulyaevi n. sp. from Palaearctic grebes

Two species of Tatria Kowalewski, 1904 are redescribed from grebes in Bulgaria: T. biremis Kowalewski, 1904 (specimens from Podiceps nigricollis) and T. minor Kowalewski, 1904 (specimens from P. cristatus and P. nigricollis). T. mircia Gulyaev, 1990 is synonymised with T. minor. The previous records of T. biremis, T. minor and T. mircia are critically analysed in view of the present results. T. gulyaevi n. sp. is described from P. nigricollis from Bulgaria and the Czech Republic and from an unidentified grebe species from Turkey. Some of the previous records of T. minor and T. biremis are recognised as belonging to T. gulyaevi. One specimen illustrated by Kowalewski (1904) is designated as a lectotype of T. minor in order to stabilise the nomenclatural standing of this species.     

Phosphatase activity during growth of Yarrowia lipolytica

Abstract The yeast Yarrowia lipolytica produces four patterns of phosphatase activity during growth in the presence or absence of inorganic phosphate in the medium. Activities had pH optima at 4.2, 5.8, about pH 6.5 and pH 9.0. The level of all four phosphatase activities depended on the presence of inorganic phosphate in the medium.     

Rhamnolipid–Biosurfactant Permeabilizing Effects on Gram-Positive and Gram-Negative Bacterial Strains

The potential of biosurfactant PS to permeabilize bacterial cells of Pseudomonas aeruginosa, Escherichia coli, and Bacillus subtilis on growing (in vivo) and resting (in vitro) cells was studied. Biosurfactant was shown to have a neutral or detrimental effect on the growth of Gram-positive strains, and this was dependent on the surfactant concentration. The growth of Gram-negative strains was not influenced by the presence of biosurfactant in the media. Cell permeabilization with biosurfactant PS was shown to be more effective with B. subtilis resting cells than with Pseudomonas aeruginosa. Scanning-electron microscopy observations showed that the biosurfactant PS did not exert a disruptive action on resting cells such that it was detrimental to the effect on growing cells of B. subtilis. Low critical micelle concentrations, tender action on nongrowing cells, and neutral effects on the growth of microbial strains at low surfactant concentrations make biosurfactant PS a potential candidate for application in different industrial fields, in environmental bioremediation, and in biomedicine.